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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ), 'gf_id' => 'HOM05D001109', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001109' ), 'data_identifier' => 'HOM05D001109', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001109', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '552', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p33590' => 'bna', 'A03p44930' => 'bna', 'A04p25620' => 'bna', 'A05p12200' => 'bna', 'A05p43080' => 'bna', 'A09p10370' => 'bna', 'A09p67810' => 'bna', 'A10p02960' => 'bna', 'Aa31LG1G20330' => 'aar', 'Aa31LG5G14790' => 'aar', 'Aa31LG5G3990' => 'aar', 'Aa31sc61G70' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.5483' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.737' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.792' => 'aag', 'Actinidia06295' => 'ach', 'Actinidia20840' => 'ach', 'Actinidia28486' => 'ach', 'Actinidia39363' => 'ach', 'Ah.04g153750' => 'amhyb', 'Ah.05g180010' => 'amhyb', 'AL1G14190' => 'aly', 'AL3G14350' => 'aly', 'AL3G45250' => 'aly', 'AL4G28970' => 'aly', 'AL6G52180' => 'aly', 'Aqoxy2G03750' => 'aox', 'Aqoxy4G00626' => 'aox', 'Aqoxy5G04035' => 'aox', 'Aqoxy7G00224' => 'aox', 'arahy.Tifrunner.gnm1.ann1.CT9WHN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E6I8MS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FNM63F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I24T5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1XP5G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDE1W9' => 'arhy', 'AT1G04540' => 'ath', 'AT2G13350' => 'ath', 'AT2G33320' => 'ath', 'AT3G04360' => 'ath', 'AT4G01200' => 'ath', 'ATR0171G015' => 'atr', 'ATR1127G210' => 'atr', 'ATR1131G044' => 'atr', 'Atru.chr2.1058' => 'acertr', 'Atru.chr4.1909' => 'acertr', 'AUR62000627' => 'cqu', 'AUR62006980' => 'cqu', 'AUR62018037' => 'cqu', 'BcaB02g10551' => 'bca', 'BcaB02g11493' => 'bca', 'BcaB03g16227' => 'bca', 'BcaB04g19339' => 'bca', 'BcaB06g28674' => 'bca', 'BcaB06g28675' => 'bca', 'BcaB08g34529' => 'bca', 'BcaC01g03125' => 'bca', 'BcaC01g04378' => 'bca', 'BcaC02g07840' => 'bca', 'BcaC02g11417' => 'bca', 'BcaC03g16059' => 'bca', 'BcaC03g16060' => 'bca', 'BcaC04g23084' => 'bca', 'BcaC04g24131' => 'bca', 'BcaC05g29947' => 'bca', 'BcaC05g30200' => 'bca', 'BcaC05g30232' => 'bca', 'BcaNung05970' => 'bca', 'BcaNung06562' => 'bca', 'BolC3t16347H' => 'bol', 'BolC3t17862H' => 'bol', 'BolC4t23147H' => 'bol', 'BolC4t23148H' => 'bol', 'BolC4t27759H' => 'bol', 'BolC5t29052H' => 'bol', 'BolC5t34938H' => 'bol', 'BolC8t52748H' => 'bol', 'BolC9t54124H' => 'bol', 'BraA03t12534Z' => 'bra', 'BraA03t13630Z' => 'bra', 'BraA04t18066Z' => 'bra', 'BraA05t20164Z' => 'bra', 'BraA05t23052Z' => 'bra', 'BraA09t36681Z' => 'bra', 'BraA09t42113Z' => 'bra', 'BraA10t42565Z' => 'bra', 'C03p40790' => 'bna', 'C03p55810' => 'bna', 'C04p15770' => 'bna', 'C04p15780' => 'bna', 'C04p62750' => 'bna', 'C05p02710' => 'bna', 'C05p62830' => 'bna', 'C08p52140' => 'bna', 'C09p12310' => 'bna', 'CAN.G29.10' => 'can', 'CAN.G484.84' => 'can', 'CAN.G524.12' => 'can', 'CAN.G566.14' => 'can', 'CAN.G638.36' => 'can', 'CAN.G78.146' => 'can', 'CAN.G802.5' => 'can', 'CANSAT54G1943' => 'cansat', 'CANSAT80G2544' => 'cansat', 'CARHR003880' => 'chi', 'CARHR078540' => 'chi', 'CARHR105170' => 'chi', 'CARHR127320' => 'chi', 'CARHR249100' => 'chi', 'Carub.0001s0375' => 'cru', 'Carub.0003s0357' => 'cru', 'Carub.0003s2788' => 'cru', 'Carub.0004s1494' => 'cru', 'Carub.0006s3624' => 'cru', 'Ca_09482_v3' => 'car', 'Ca_09798_v3' => 'car', 'Ca_10023_v3' => 'car', 'Ca_11881_v3' => 'car', 'Cc00_g01750' => 'ccan', 'Cc02_g38800' => 'ccan', 'Cc03_g06390' => 'ccan', 'Cc09_g02890' => 'ccan', 'Cc09_g02900' => 'ccan', 'CDE05G0127' => 'cde', 'CDE05G0985' => 'cde', 'CDE08G0587' => 'cde', 'Cfa003850' => 'cfa', 'Cfa006376' => 'cfa', 'Cfa014787' => 'cfa', 'Ciclev10006849m.g' => 'ccl', 'Ciclev10021815m.g' => 'ccl', 'Ciclev10033675m.g' => 'ccl', 'CiPaw.01G177400' => 'cil', 'CiPaw.02G037300' => 'cil', 'CiPaw.02G106600' => 'cil', 'CiPaw.07G071400' => 'cil', 'ClCG11G010410' => 'cla', 'COL.COLO4_06359' => 'col', 'COL.COLO4_15517' => 'col', 'COL.COLO4_15972' => 'col', 'COL.COLO4_29200' => 'col', 'Cpa.g.sc184.8' => 'cpa', 'Cpa.g.sc59.5' => 'cpa', 'Cpa.g.sc717.2' => 'cpa', 'CsaV3_2G009950' => 'csa', 'CsaV3_2G012410' => 'csa', 'CsaV3_3G008290' => 'csa', 'CSS0007005' => 'camsi', 'CSS0011580' => 'camsi', 'CSS0022080' => 'camsi', 'CSS0037425' => 'camsi', 'CSS0041011' => 'camsi', 'DCAR_003923' => 'dca', 'DCAR_007036' => 'dca', 'DCAR_021437' => 'dca', 'DCAR_023880' => 'dca', 'DCAR_024294' => 'dca', 'DCAR_025234' => 'dca', 'DCAR_028377' => 'dca', 'Dinv11438' => 'din', 'Dinv21641' => 'din', 'Dinv24656' => 'din', 'Dinv27118' => 'din', 'Dinv29799' => 'din', 'Dinv31709' => 'din', 'Dinv32272' => 'din', 'Duzib052G0388' => 'dzi', 'Duzib106G0605' => 'dzi', 'Duzib106G0960' => 'dzi', 'Duzib128G1097' => 'dzi', 'Duzib138G0142' => 'dzi', 'Duzib147G0373' => 'dzi', 'Duzib147G0441' => 'dzi', 'Duzib147G1116' => 'dzi', 'Duzib151G0667' => 'dzi', 'Duzib160G0840' => 'dzi', 'Duzib177G0452' => 'dzi', 'Duzib212G0265' => 'dzi', 'Duzib264G0146' => 'dzi', 'Duzib268G1206' => 'dzi', 'ECA234G3673' => 'eca', 'EL10Ac1g00332' => 'bvu', 'EL10Ac3g06676' => 'bvu', 'EL10Ac4g09751' => 'bvu', 'Eucgr.B02156' => 'egr', 'Eucgr.E00081' => 'egr', 'Eucgr.H00123' => 'egr', 'Eucgr.H00124' => 'egr', 'Eucgr.H00125' => 'egr', 'Eucgr.H02915' => 'egr', 'FAN01G2402' => 'fan', 'FAN03G1135' => 'fan', 'FAN05G0479' => 'fan', 'FAN06G0693' => 'fan', 'FAN06G2199' => 'fan', 'FAN09G2682' => 'fan', 'FAN10G0645' => 'fan', 'FAN10G2442' => 'fan', 'FAN12G2240' => 'fan', 'FAN12G2413' => 'fan', 'FAN14G4077' => 'fan', 'FAN14G5291' => 'fan', 'FAN16G1055' => 'fan', 'FAN17G2697' => 'fan', 'FAN22G2368' => 'fan', 'FvH4_3g05810' => 'fve', 'FvH4_4g04680' => 'fve', 'FvH4_6g01610' => 'fve', 'FvH4_7g15700' => 'fve', 'Glyma.03G249700' => 'gma', 'Glyma.03G254400' => 'gma', 'Glyma.10G130100' => 'gma', 'Glyma.10G165300' => 'gma', 'Glyma.19G247300' => 'gma', 'Glyma.19G252000' => 'gma', 'Glyma.20G081900' => 'gma', 'Glyma.20G199700' => 'gma', 'Gohir.A02G043300' => 'ghi', 'Gohir.A05G149500' => 'ghi', 'Gohir.A06G190200' => 'ghi', 'Gohir.A08G217700' => 'ghi', 'Gohir.A08G221618' => 'ghi', 'Gohir.A09G227300' => 'ghi', 'Gohir.A10G107250' => 'ghi', 'Gohir.A11G093350' => 'ghi', 'Gohir.A11G245600' => 'ghi', 'Gohir.A11G299600' => 'ghi', 'Gohir.A12G110100' => 'ghi', 'Gohir.D02G049000' => 'ghi', 'Gohir.D05G152100' => 'ghi', 'Gohir.D06G198600' => 'ghi', 'Gohir.D08G234700' => 'ghi', 'Gohir.D09G228300' => 'ghi', 'Gohir.D11G255901' => 'ghi', 'Gohir.D11G314500' => 'ghi', 'Gohir.D12G113100' => 'ghi', 'Gorai.004G249500' => 'gra', 'Gorai.004G254600' => 'gra', 'Gorai.005G054200' => 'gra', 'Gorai.006G251000' => 'gra', 'Gorai.007G274200' => 'gra', 'Gorai.007G345600' => 'gra', 'Gorai.008G122700' => 'gra', 'Gorai.009G156100' => 'gra', 'Gorai.010G231500' => 'gra', 'Gorai.011G179900' => 'gra', 'GSVIVG01027920001' => 'vvi', 'HanXRQChr16g0523831' => 'han', 'HanXRQChr17g0561051' => 'han', 'Haze_04403' => 'cav', 'Haze_05574' => 'cav', 'Haze_11207' => 'cav', 'Haze_11464' => 'cav', 'Haze_15600' => 'cav', 'Hma1.2p1_0384F.1_g140860' => 'hma', 'Hma1.2p1_0385F.1_g141610' => 'hma', 'Hma1.2p1_1336F.1_g276450' => 'hma', 'Hma1.2p1_1336F.1_g276455' => 'hma', 'Hma1.2p1_1336F.1_g276460' => 'hma', 'HPP92_005114' => 'vpl', 'HPP92_005509' => 'vpl', 'HPP92_022477' => 'vpl', 'HPP92_025828' => 'vpl', 'Lalb_Chr01g0011371' => 'lal', 'Lalb_Chr02g0149011' => 'lal', 'Lalb_Chr04g0262131' => 'lal', 'Lalb_Chr06g0169551' => 'lal', 'Lalb_Chr19g0128541' => 'lal', 'Lalb_Chr21g0311141' => 'lal', 'Lalb_Chr21g0312521' => 'lal', 'Lj1g0002783' => 'lja', 'Lj1g0016035' => 'lja', 'Lj2C45T1' => 'lonja', 'Lj2C45T9' => 'lonja', 'Lj5g0018161' => 'lja', 'Lj5g0018572' => 'lja', 'Lj6A620T53' => 'lonja', 'Lj6g0026573' => 'lja', 'Lj7P505T16' => 'lonja', 'Lj8P197T23' => 'lonja', 'Lsat_1_v5_gn_0_42241' => 'lsa', 'Lsat_1_v5_gn_4_34140' => 'lsa', 'Lsat_1_v5_gn_5_79441' => 'lsa', 'Manes.01G250700' => 'mes', 'Manes.03G054250' => 'mes', 'Manes.03G056817' => 'mes', 'Manes.03G158400' => 'mes', 'Manes.06G171500' => 'mes', 'Manes.08G140600' => 'mes', 'Manes.09G147300' => 'mes', 'Manes.15G046100' => 'mes', 'Mapoly0005s0112' => 'mpo', 'Mapoly0005s0113' => 'mpo', 'Mapoly0015s0136' => 'mpo', 'Mapoly0104s0027' => 'mpo', 'Mapoly0133s0012' => 'mpo', 'Mapoly0163s0014' => 'mpo', 'MapolyY_B0012' => 'mpo', 'MapolyY_B0034' => 'mpo', 'MBI06_g04299_MAGBIO' => 'mbi', 'MD00G1149000' => 'mdo', 'MD01G1073700' => 'mdo', 'MD03G1187600' => 'mdo', 'MD04G1232000' => 'mdo', 'MD05G1286300' => 'mdo', 'MD05G1359000' => 'mdo', 'MD13G1222100' => 'mdo', 'MD13G1272000' => 'mdo', 'MD15G1341600' => 'mdo', 'MD16G1227000' => 'mdo', 'Medtr1g045780' => 'mtr', 'Medtr1g073210' => 'mtr', 'Medtr1g080360' => 'mtr', 'Medtr7g115480' => 'mtr', 'Medtr7g116840' => 'mtr', 'MELO3C006047.2' => 'cme', 'MELO3C008645.2' => 'cme', 'MELO3C023045.2' => 'cme', 'Migut.F01811' => 'egut', 'Migut.F02060' => 'egut', 'Migut.F02061' => 'egut', 'Migut.F02062' => 'egut', 'Migut.G00573' => 'egut', 'Migut.N00304' => 'egut', 'Migut.N01575' => 'egut', 'MSTRG.27437' => 'ama', 'MSTRG.4176' => 'ama', 'MSTRG.4826' => 'ama', 'MSTRG.9214' => 'ama', 'MSTRG.9215' => 'ama', 'Nitab4.5_0000061g0060' => 'nta', 'Nitab4.5_0000061g0080' => 'nta', 'Nitab4.5_0000305g0300' => 'nta', 'Nitab4.5_0000355g0010' => 'nta', 'Nitab4.5_0000476g0230' => 'nta', 'Nitab4.5_0000592g0410' => 'nta', 'Nitab4.5_0001040g0010' => 'nta', 'Nitab4.5_0001655g0070' => 'nta', 'Nitab4.5_0002210g0030' => 'nta', 'Nitab4.5_0006344g0010' => 'nta', 'Nitab4.5_0006471g0020' => 'nta', 'Nitab4.5_0007224g0010' => 'nta', 'Nitab4.5_0008375g0040' => 'nta', 'Nitab4.5_0010891g0020' => 'nta', 'Nitab4.5_0013021g0020' => 'nta', 'Nn1g02966' => 'nnu', 'Nn1g03287' => 'nnu', 'Nn1g04397' => 'nnu', 'Nn1g08095' => 'nnu', 'Nn1g09341' => 'nnu', 'Nn3g19788' => 'nnu', 'Nn3g20695' => 'nnu', 'Nn4g22409' => 'nnu', 'Nn4g26541' => 'nnu', 'Nn6g33272' => 'nnu', 'Nn6g34872' => 'nnu', 'Nn7g37339' => 'nnu', 'Oeu001249.1' => 'oeu', 'Oeu004922.1' => 'oeu', 'Oeu007694.1' => 'oeu', 'Oeu011213.1' => 'oeu', 'Oeu030913.1' => 'oeu', 'Oeu051338.1' => 'oeu', 'Oeu051339.1' => 'oeu', 'Oeu055046.1' => 'oeu', 'Oeu055261.1' => 'oeu', 'Oeu059394.1' => 'oeu', 'Os01g0659800' => 'osa', 'Os02g0815100' => 'osa', 'Peaxi162Scf00156g00922' => 'pax', 'Peaxi162Scf00169g00223' => 'pax', 'Peaxi162Scf00319g00522' => 'pax', 'Peaxi162Scf00373g00122' => 'pax', 'Peaxi162Scf00373g01211' => 'pax', 'Peaxi162Scf00498g00734' => 'pax', 'Peaxi162Scf01044g00227' => 'pax', 'Peaxi162Scf01367g00004' => 'pax', 'PGR004G1508' => 'pgr', 'PGR031G2213' => 'pgr', 'PGR031G3366' => 'pgr', 'PGR042G3249' => 'pgr', 'PGR119G0165' => 'pgr', 'PGR142G0466' => 'pgr', 'PGSC0003DMG400000080' => 'stu', 'PGSC0003DMG400001497' => 'stu', 'PGSC0003DMG400004139' => 'stu', 'PGSC0003DMG400008289' => 'stu', 'PGSC0003DMG400013409' => 'stu', 'PGSC0003DMG400029340' => 'stu', 'PGSC0003DMG400030915' => 'stu', 'Phvul.006G104400' => 'pvu', 'Phvul.006G109100' => 'pvu', 'Phvul.007G232100' => 'pvu', 'Phvul.011G087700' => 'pvu', 'Phvul.011G087800' => 'pvu', 'Phvul.011G133560' => 'pvu', 'Potri.001G458101' => 'ptr', 'Potri.002G166400' => 'ptr', 'Potri.008G172300' => 'ptr', 'Potri.010G065300' => 'ptr', 'Potri.013G048400' => 'ptr', 'Potri.019G021300' => 'ptr', 'Pp3c12_16910' => 'ppa', 'Pp3c14_12090' => 'ppa', 'Pp3c18_18780' => 'ppa', 'Pp3c21_10380' => 'ppa', 'Pp3c21_12250' => 'ppa', 'Pp3c22_3410' => 'ppa', 'Pp3c2_20180' => 'ppa', 'Pp3c3_32730' => 'ppa', 'Pp3c4_8950' => 'ppa', 'Prupe.1G049100' => 'ppe', 'Prupe.2G181800' => 'ppe', 'Prupe.4G078600' => 'ppe', 'Prupe.6G351400' => 'ppe', 'Psat0s3161g0120' => 'psa', 'Psat3g004720' => 'psa', 'Psat6g107680' => 'psa', 'Psat6g131240' => 'psa', 'Psat6g144280' => 'psa', 'PSO135G0220' => 'pso', 'PSO339G6679' => 'pso', 'PSO384G0759' => 'pso', 'PSO384G1343' => 'pso', 'PSO541G3564' => 'pso', 'PSO675G8536' => 'pso', 'QL03p029650' => 'qlo', 'QL04p058872' => 'qlo', 'QL06p021159' => 'qlo', 'QL07p036215' => 'qlo', 'RcHm_v2.0_Chr1g0358431' => 'rch', 'RcHm_v2.0_Chr3g0449421' => 'rch', 'RcHm_v2.0_Chr4g0395501' => 'rch', 'RcHm_v2.0_Chr5g0013681' => 'rch', 'Rhsim01G0168900' => 'rsi', 'Rhsim01G0185800' => 'rsi', 'Rhsim02G0044200' => 'rsi', 'Rhsim04G0171700' => 'rsi', 'Rhsim09G0133400' => 'rsi', 'Sabra02G0145200' => 'sbr', 'Sabra08G0131600' => 'sbr', 'Sabra10G0041800' => 'sbr', 'Sabra11G0128000' => 'sbr', 'Sabra13G0044500' => 'sbr', 'Sabra19G0032900' => 'sbr', 'SalBow1G1684' => 'sbo', 'SalBow1G2040' => 'sbo', 'SalBow1G2365' => 'sbo', 'SalBow1G5146' => 'sbo', 'SalBow1G6404' => 'sbo', 'SalBow1G8496' => 'sbo', 'SalBow2G2832' => 'sbo', 'SalBow3G0670' => 'sbo', 'SalBow3G1864' => 'sbo', 'SalBow3G4474' => 'sbo', 'SalBow5G1095' => 'sbo', 'Sc01g0003090' => 'sci', 'Sc11g0008450' => 'sci', 'Sc16g0009820' => 'sci', 'Sc19g0005570' => 'sci', 'Sc25g0004830' => 'sci', 'Sed0001218' => 'sed', 'Sed0005987' => 'sed', 'Sed0013569' => 'sed', 'Sed0026722' => 'sed', 'SEGI_26923' => 'sgi', 'SEGI_31534' => 'sgi', 'SGA_v2.0_scaffold31G12625' => 'sas', 'SGA_v2.0_scaffold577G53012' => 'sas', 'SGA_v2.0_scaffold62G21461' => 'sas', 'SGA_v2.0_scaffold62G21464' => 'sas', 'SGA_v2.0_scaffold67G22678' => 'sas', 'SGA_v2.0_scaffold71G24041' => 'sas', 'SHI00854' => 'shi', 'SHI14673' => 'shi', 'SMO115G0119' => 'smo', 'SMO172G0022' => 'smo', 'SMO198G0028' => 'smo', 'SMO340G0080' => 'smo', 'SMO340G0289' => 'smo', 'SMO351G0155' => 'smo', 'SMO356G0014' => 'smo', 'Solyc01g095360.2' => 'sly', 'Solyc02g070690.1' => 'sly', 'Solyc03g005720.3' => 'sly', 'Solyc04g050130.1' => 'sly', 'Solyc05g055920.4' => 'sly', 'Solyc07g008070.1' => 'sly', 'Solyc09g090920.4' => 'sly', 'Solyc12g096970.2' => 'sly', 'Sopen01g039130' => 'spe', 'Sopen02g019770' => 'spe', 'Sopen03g001730' => 'spe', 'Sopen04g020800' => 'spe', 'Sopen05g034320' => 'spe', 'Sopen07g003950' => 'spe', 'Sopen09g033870' => 'spe', 'Sopen09g033900' => 'spe', 'Sopen12g032780' => 'spe', 'Sp1g03370' => 'spa', 'Sp3g03260' => 'spa', 'Sp3g26820' => 'spa', 'Sp4g15630' => 'spa', 'Sp6g00920' => 'spa', 'TAR330G0002' => 'tar', 'TAR362G0921' => 'tar', 'TAR626G0001' => 'tar', 'TAR626G0715' => 'tar', 'TAR633G2760' => 'tar', 'THA.LOC104801063' => 'tha', 'THA.LOC104809022' => 'tha', 'THA.LOC104817045' => 'tha', 'THA.LOC104826097' => 'tha', 'THA.LOC104826528' => 'tha', 'THA.LOC104827356' => 'tha', 'THA.LOC104827473' => 'tha', 'Thecc.01G349500' => 'tca', 'Thecc.04G025400' => 'tca', 'Thecc.04G036800' => 'tca', 'Thecc.04G265500' => 'tca', 'Thecc.06G152600' => 'tca', 'Thhalv10007144m.g' => 'esa', 'Thhalv10016412m.g' => 'esa', 'Thhalv10020890m.g' => 'esa', 'Thhalv10022712m.g' => 'esa', 'Thhalv10028892m.g' => 'esa', 'TPR.G18551' => 'tpr', 'TPR.G23988' => 'tpr', 'TPR.G26639' => 'tpr', 'TPR.G34428' => 'tpr', 'TPR.G4700' => 'tpr', 'TPR.G6909' => 'tpr', 'TPR.G6948' => 'tpr', 'TWI09G1084' => 'twi', 'TWI32G0237' => 'twi', 'TWI34G0760' => 'twi', 'TWI36G1547' => 'twi', 'TWI53G0064' => 'twi', 'TWI60G0626' => 'twi', 'TWI60G0806' => 'twi', 'unitig_8.g3340' => 'ugi', 'vmacro08557' => 'vma', 'vmacro10380' => 'vma', 'vmacro15482' => 'vma', 'vmacro20871' => 'vma', 'VMungo0540G1223' => 'vmu', 'VMungo0540G1579' => 'vmu', 'VMungo0720G0550' => 'vmu', 'VMungo0720G1348' => 'vmu', 'VMungo1215G1036' => 'vmu', 'Zm00001eb157840' => 'zma', 'Zm00001eb191520' => 'zma' ) $gf_id = 'HOM05D001109' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001109' ) $data_identifier = 'HOM05D001109' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 3, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 4, 'ccan' => (int) 5, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 4, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 7, 'din' => (int) 7, 'dzi' => (int) 14, 'eca' => (int) 1, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 8, 'ghi' => (int) 19, 'gra' => (int) 10, 'vvi' => (int) 1, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 5, 'lonja' => (int) 5, 'lsa' => (int) 3, 'mes' => (int) 8, 'mpo' => (int) 8, 'mbi' => (int) 1, 'mdo' => (int) 10, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 7, 'ama' => (int) 5, 'nta' => (int) 15, 'nnu' => (int) 12, 'oeu' => (int) 10, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 6, 'stu' => (int) 7, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 9, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 6, 'sbo' => (int) 11, 'sci' => (int) 5, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 6, 'shi' => (int) 2, 'smo' => (int) 7, 'sly' => (int) 8, 'spe' => (int) 9, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 7, 'tca' => (int) 5, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 7, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb191520' $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